package eu.etaxonomy.cdm.model.name;
-
import eu.etaxonomy.cdm.model.occurrence.Specimen;
import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
import eu.etaxonomy.cdm.model.reference.ReferenceBase;
import eu.etaxonomy.cdm.model.taxon.Synonym;
import eu.etaxonomy.cdm.model.taxon.Taxon;
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
+import eu.etaxonomy.cdm.model.common.IParsable;
+import eu.etaxonomy.cdm.model.common.IRelated;
import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
import eu.etaxonomy.cdm.model.common.IReferencedEntity;
+import eu.etaxonomy.cdm.model.common.RelationshipBase;
+
+
import org.apache.log4j.Logger;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
+import org.hibernate.annotations.Index;
+import org.hibernate.annotations.Target;
+
+import eu.etaxonomy.cdm.strategy.cache.INameCacheStrategy;
-import eu.etaxonomy.cdm.strategy.INameCacheStrategy;
+
+import java.lang.reflect.Method;
import java.util.*;
import javax.persistence.*;
/**
- * The upmost (abstract) class for scientific taxon names regardless of the any
- * particular nomenclatural code. The scientific name including author strings and
- * maybe year is stored in IdentifiableEntity.titleCache
+ * The upmost (abstract) class for scientific taxon names regardless of any
+ * particular nomenclature code. The scientific taxon name does not depend
+ * on the use made of it in a publication or a treatment
+ * ({@link taxon.TaxonBase taxon concept respectively potential taxon})
+ * as an {@link taxon.Taxon "accepted" respectively "correct" (taxon) name}
+ * or as a {@link taxon.Synonym synonym}.
+ *
* @author m.doering
* @version 1.0
* @created 08-Nov-2007 13:06:57
*/
@Entity
@Inheritance(strategy=InheritanceType.SINGLE_TABLE)
-public abstract class TaxonNameBase extends IdentifiableEntity<TaxonNameBase> implements IReferencedEntity {
+public abstract class TaxonNameBase<T extends TaxonNameBase, S extends INameCacheStrategy> extends IdentifiableEntity<TaxonNameBase> implements IReferencedEntity, IParsable, IRelated {
static Logger logger = Logger.getLogger(TaxonNameBase.class);
- //The scientific name without author strings and year
- private String nameCache;
- //Non-atomised addition to a name not ruled by a nomenclatural code
private String appendedPhrase;
- //Details of the nomenclatural reference (protologue). These are mostly (implicitly) pages but can also be figures or
- //tables or any other element of a publication. {only if a nomenclatural reference exists}
private String nomenclaturalMicroReference;
- //this flag will be set to true if the parseName method was unable to successfully parse the name
private boolean hasProblem = false;
- protected Set<NameTypeDesignation> nameTypeDesignations = new HashSet();
+ protected Set<NameTypeDesignation> nameTypeDesignations = new HashSet<NameTypeDesignation>();
+ private Set<SpecimenTypeDesignation> specimenTypeDesignations = new HashSet<SpecimenTypeDesignation>();
private HomotypicalGroup homotypicalGroup = new HomotypicalGroup();
- private Set<NameRelationship> nameRelations = new HashSet();
- private Set<NomenclaturalStatus> status = new HashSet();
+ private Set<NameRelationship> relationsFromThisName = new HashSet<NameRelationship>();
+ private Set<NameRelationship> relationsToThisName = new HashSet<NameRelationship>();
+ private Set<NomenclaturalStatus> status = new HashSet<NomenclaturalStatus>();
+ private Set<TaxonBase> taxonBases = new HashSet<TaxonBase>();
private Rank rank;
- //if set, the Reference.isNomenclaturallyRelevant flag should be set to true!
private INomenclaturalReference nomenclaturalReference;
- private Set<TaxonNameBase> newCombinations = new HashSet();
- // bidrectional with newCombinations. Keep congruent
- private TaxonNameBase basionym;
-
- protected INameCacheStrategy cacheStrategy;
+ static Method methodTaxonBaseSetName;
- // CONSTRUCTORS
+// ************* CONSTRUCTORS *************/
+ /**
+ * Class constructor: creates a new empty taxon name.
+ *
+ * @see #TaxonNameBase(Rank)
+ * @see #TaxonNameBase(HomotypicalGroup)
+ * @see #TaxonNameBase(Rank, HomotypicalGroup)
+ */
public TaxonNameBase() {
- super();
+ this(null, null);
}
+ /**
+ * Class constructor: creates a new taxon name
+ * only containing its {@link common.Rank rank}.
+ *
+ * @param rank the rank to be assigned to this taxon name
+ * @see #TaxonNameBase()
+ * @see #TaxonNameBase(HomotypicalGroup)
+ * @see #TaxonNameBase(Rank, HomotypicalGroup)
+ */
public TaxonNameBase(Rank rank) {
+ this(rank, null);
+ }
+ /**
+ * Class constructor: creates a new taxon name
+ * only containing its {@link common.HomotypicalGroup homotypical group}.
+ * The new taxon name will be also added to the set of taxon names
+ * belonging to this homotypical group. If the homotypical group
+ * does not exist a new instance will be created for it.
+ *
+ * @param homotypicalGroup the homotypical group to which this taxon name belongs
+ * @see #TaxonNameBase()
+ * @see #TaxonNameBase(Rank)
+ * @see #TaxonNameBase(Rank, HomotypicalGroup)
+ */
+ public TaxonNameBase(HomotypicalGroup homotypicalGroup) {
+ this(null, homotypicalGroup);
+ }
+ /**
+ * Class constructor: creates a new taxon name
+ * only containing its {@link common.Rank rank} and
+ * its {@link common.HomotypicalGroup homotypical group}.
+ *
+ * @param rank the rank to be assigned to this taxon name
+ * @param homotypicalGroup the homotypical group to which this taxon name belongs
+ * @see #TaxonNameBase()
+ * @see #TaxonNameBase(Rank)
+ * @see #TaxonNameBase(HomotypicalGroup)
+ */
+ public TaxonNameBase(Rank rank, HomotypicalGroup homotypicalGroup) {
super();
this.setRank(rank);
+ if (homotypicalGroup == null){
+ homotypicalGroup = new HomotypicalGroup();
+ }
+ homotypicalGroup.addTypifiedName(this);
}
-
- public String getNameCache() {
- return nameCache;
- }
- public void setNameCache(String nameCache) {
- this.nameCache = nameCache;
- }
-
+//********* METHODS **************************************/
+ //@Index(name="TaxonNameBaseTitleCacheIndex")
+// public String getTitleCache(){
+// return super.getTitleCache();
+// }
+
+ /**
+ * Returns the boolean value "true" if the components of this taxon name
+ * follow the rules of the corresponding {@link NomenclaturalCode nomenclatural code},
+ * "false" otherwise. The nomenclature code depends on
+ * the concrete name subclass ({@link BacterialName BacterialName},
+ * {@link BotanicalName BotanicalName}, {@link CultivarPlantName CultivarPlantName},
+ * {@link ZoologicalName ZoologicalName} or {@link ViralName ViralName})
+ * to which this taxon name belongs.
+ *
+ * @return the boolean value expressing the compliance of this taxon name to the nomenclatural code
+ */
@Transient
public abstract boolean isCodeCompliant();
- @OneToMany
- @Cascade({CascadeType.SAVE_UPDATE})
+ /**
+ * Returns the set of all {@link NameRelationship name relationships}
+ * in which this taxon name is involved. A taxon name can be both source
+ * in some name relationships or target in some others.
+ *
+ * @see #getRelationsToThisName()
+ * @see #getRelationsFromThisName()
+ * @see #addNameRelationship(NameRelationship)
+ * @see #addRelationshipToName(TaxonNameBase, NameRelationshipType, String)
+ * @see #addRelationshipFromName(TaxonNameBase, NameRelationshipType, String)
+ */
+ @Transient
public Set<NameRelationship> getNameRelations() {
- return nameRelations;
+ Set<NameRelationship> rels = new HashSet<NameRelationship>();
+ rels.addAll(getRelationsFromThisName());
+ rels.addAll(getRelationsToThisName());
+ return rels;
+ }
+ /**
+ * Creates a new {@link NameRelationship#NameRelationship(TaxonNameBase, TaxonNameBase, NameRelationshipType, String) name relationship} from this taxon name to another taxon name
+ * and adds it both to the set of {@link #getRelationsFromThisName() relations from this taxon name} and
+ * to the set of {@link #getRelationsToThisName() relations to the other taxon name}.
+ *
+ * @param toName the taxon name of the target for this new name relationship
+ * @param type the type of this new name relationship
+ * @param ruleConsidered the string which specifies the rule on which this name relationship is based
+ * @see #getRelationsToThisName()
+ * @see #getNameRelations()
+ * @see #addRelationshipFromName(TaxonNameBase, NameRelationshipType, String)
+ * @see #addNameRelationship(NameRelationship)
+ */
+ public void addRelationshipToName(TaxonNameBase toName, NameRelationshipType type, String ruleConsidered){
+ NameRelationship rel = new NameRelationship(toName, this, type, ruleConsidered);
}
- protected void setNameRelations(Set<NameRelationship> nameRelations) {
- this.nameRelations = nameRelations;
+ /**
+ * Creates a new {@link NameRelationship#NameRelationship(TaxonNameBase, TaxonNameBase, NameRelationshipType, String) name relationship} from another taxon name to this taxon name
+ * and adds it both to the set of {@link #getRelationsToThisName() relations to this taxon name} and
+ * to the set of {@link #getRelationsFromThisName() relations from the other taxon name}.
+ *
+ * @param fromName the taxon name of the source for this new name relationship
+ * @param type the type of this new name relationship
+ * @param ruleConsidered the string which specifies the rule on which this name relationship is based
+ * @see #getRelationsFromThisName()
+ * @see #getNameRelations()
+ * @see #addRelationshipToName(TaxonNameBase, NameRelationshipType, String)
+ * @see #addNameRelationship(NameRelationship)
+ */
+ public void addRelationshipFromName(TaxonNameBase fromName, NameRelationshipType type, String ruleConsidered){
+ NameRelationship rel = new NameRelationship(this, fromName, type, ruleConsidered);
}
- public void addNameRelation(NameRelationship nameRelation) {
- // checks whether this is a normal relation or an inverse one
- // and adds it to the appropiate set
- //this.inverseNameRelations
- this.nameRelations.add(nameRelation);
+ /**
+ * Adds an existing {@link NameRelationship name relationship} either to the set of
+ * {@link #getRelationsToThisName() relations to this taxon name} or to the set of
+ * {@link #getRelationsFromThisName() relations from this taxon name}. If neither the
+ * source nor the target of the name relationship match with this taxon
+ * no addition will be carried out.
+ *
+ * @param rel the name relationship to be added to one of this taxon name's name relationships sets
+ * @see #getNameRelations()
+ * @see #addRelationshipToName(TaxonNameBase, NameRelationshipType, String)
+ * @see #addRelationshipFromName(TaxonNameBase, NameRelationshipType, String)
+ */
+ protected void addNameRelationship(NameRelationship rel) {
+ if (rel!=null && rel.getToName().equals(this)){
+ this.relationsToThisName.add(rel);
+ }else if(rel!=null && rel.getFromName().equals(this)){
+ this.relationsFromThisName.add(rel);
+ }else{
+ //TODO: raise error???
+ }
}
- public void removeNameRelation(NameRelationship nameRelation) {
- // this.inverseNameRelations
- this.nameRelations.remove(nameRelation);
+ /**
+ * Removes one {@link NameRelationship name relationship} from one of both sets of
+ * {@link #getNameRelations() name relationships} in which this taxon name is involved.
+ * The name relationship will also be removed from one of both sets belonging
+ * to the second taxon name involved. Furthermore the fromName and toName
+ * attributes of the name relationship object will be nullified.
+ *
+ * @param nameRelation the name relationship which should be deleted from one of both sets
+ * @see #getNameRelations()
+ */
+ public void removeNameRelationship(NameRelationship nameRelation) {
+ //TODO to be implemented?
+ logger.warn("not yet fully implemented?");
+ this.relationsToThisName.remove(nameRelation);
+ this.relationsFromThisName.remove(nameRelation);
}
- @Transient
- public Set<NameRelationship> getIncomingNameRelations() {
- // FIXME: filter relations
- return nameRelations;
- }
- @Transient
- public Set<NameRelationship> getOutgoingNameRelations() {
- // FIXME: filter relations
- return nameRelations;
+ public void addRelationship(RelationshipBase relation) {
+ if (relation instanceof NameRelationship){
+ addNameRelationship((NameRelationship)relation);
+ }else{
+ //TODO exception handling
+ }
}
-
- @OneToMany
+ /**
+ * Returns the set of all {@link NameRelationship name relationships}
+ * in which this taxon name is involved as a source.
+ *
+ * @see #getNameRelations()
+ * @see #getRelationsToThisName()
+ * @see #addRelationshipFromName(TaxonNameBase, NameRelationshipType, String)
+ */
+ @OneToMany(mappedBy="relatedFrom", fetch= FetchType.EAGER)
@Cascade({CascadeType.SAVE_UPDATE})
- public Set<NomenclaturalStatus> getStatus() {
- return status;
+ public Set<NameRelationship> getRelationsFromThisName() {
+ return relationsFromThisName;
}
- protected void setStatus(Set<NomenclaturalStatus> status) {
- this.status = status;
+ private void setRelationsFromThisName(Set<NameRelationship> relationsFromThisName) {
+ this.relationsFromThisName = relationsFromThisName;
}
- public void addStatus(NomenclaturalStatus status) {
- this.status.add(status);
+
+ /**
+ * Returns the set of all {@link NameRelationship name relationships}
+ * in which this taxon name is involved as a target.
+ *
+ * @see #getNameRelations()
+ * @see #getRelationsFromThisName()
+ * @see #addRelationshipToName(TaxonNameBase, NameRelationshipType, String)
+ */
+ @OneToMany(mappedBy="relatedTo", fetch= FetchType.EAGER)
+ @Cascade({CascadeType.SAVE_UPDATE})
+ public Set<NameRelationship> getRelationsToThisName() {
+ return relationsToThisName;
}
- public void removeStatus(NomenclaturalStatus status) {
- this.status.remove(status);
+ private void setRelationsToThisName(Set<NameRelationship> relationsToThisName) {
+ this.relationsToThisName = relationsToThisName;
}
-
-
- @OneToMany
+
+ /**
+ * Returns the set of {@link NomenclaturalStatus nomenclatural status} assigned
+ * to this taxon name according to its corresponding nomenclature code.
+ * This includes the {@link NomenclaturalStatusType type} of the nomenclatural status
+ * and the nomenclatural code rule considered.
+ *
+ * @see NomenclaturalStatus
+ * @see NomenclaturalStatusType
+ */
+ @OneToMany(fetch= FetchType.EAGER)
@Cascade({CascadeType.SAVE_UPDATE})
- public Set<TaxonNameBase> getNewCombinations() {
- return newCombinations;
+ public Set<NomenclaturalStatus> getStatus() {
+ return status;
}
- protected void setNewCombinations(Set<TaxonNameBase> newCombinations) {
- this.newCombinations = newCombinations;
+ /**
+ * @see #getStatus()
+ */
+ protected void setStatus(Set<NomenclaturalStatus> nomStatus) {
+ this.status = nomStatus;
+ }
+ /**
+ * Adds a new {@link NomenclaturalStatus nomenclatural status}
+ * to this taxon name's set of nomenclatural status.
+ *
+ * @param nomStatus the nomenclatural status to be added
+ * @see #getStatus()
+ */
+ public void addStatus(NomenclaturalStatus nomStatus) {
+ this.status.add(nomStatus);
+ }
+ /**
+ * Removes one element from the set of nomenclatural status of this taxon name.
+ * Type and ruleConsidered attributes of the nomenclatural status object
+ * will be nullified.
+ *
+ * @param nomStatus the nomenclatural status of this taxon name which should be deleted
+ * @see #getStatus()
+ */
+ public void removeStatus(NomenclaturalStatus nomStatus) {
+ //TODO to be implemented?
+ logger.warn("not yet fully implemented?");
+ this.status.remove(nomStatus);
}
- public void addNewCombination(TaxonNameBase newCombination) {
- // TODO: add basionym relation too!
- this.newCombinations.add(newCombination);
+
+
+ /**
+ * Indicates if this taxon name is a {@link NameRelationshipType.BASIONYM() basionym}
+ * or a {@link NameRelationshipType.REPLACED_SYNONYM() replaced synonym}
+ * of any other taxon name. Returns true, if a basionym or a replaced synonym
+ * relationship from this taxon name to another taxon name exists,
+ * false otherwise (also in case this taxon name is the only one in the
+ * homotypical group).
+ */
+ @Transient
+ public boolean isOriginalCombination(){
+ Set<NameRelationship> relationsFromThisName = this.getRelationsFromThisName();
+ for (NameRelationship relation : relationsFromThisName) {
+ if (relation.getType().equals(NameRelationshipType.BASIONYM()) ||
+ relation.getType().equals(NameRelationshipType.REPLACED_SYNONYM())) {
+ return true;
+ }
+ }
+ return false;
}
- public void removeNewCombination(TaxonNameBase newCombination) {
- this.newCombinations.remove(newCombination);
+
+ /**
+ * Returns the taxon name which is the {@link NameRelationshipType.BASIONYM() basionym} of this taxon name.
+ * The basionym of a taxon name is its epithet-bringing synonym.
+ * For instance Pinus abies L. was published by Linnaeus and the botanist
+ * Karsten transferred later this taxon to the genus Picea. Therefore,
+ * Pinus abies L. is the basionym of the new combination Picea abies (L.) H. Karst.
+ */
+ @Transient
+ public T getBasionym(){
+ //TODO: pick the right name relationships...
+ return null;
}
-
-
- @ManyToOne
- @Cascade({CascadeType.SAVE_UPDATE})
- public TaxonNameBase getBasionym(){
- return this.basionym;
+ /**
+ * Assigns another taxon name as {@link NameRelationshipType.BASIONYM() basionym} of this taxon name.
+ * The basionym relationship will be added to this taxon name
+ * and to the basionym. The basionym cannot have itself a basionym.
+ *
+ * @see #getBasionym()
+ * @see #setBasionym(TaxonNameBase, String)
+ */
+ public void setBasionym(T basionym){
+ setBasionym(basionym, null);
}
- public void setBasionym(TaxonNameBase basionym){
- // TODO: add newCombination relation too!
- this.basionym = basionym;
+ /**
+ * Assigns another taxon name as {@link NameRelationshipType.BASIONYM() basionym} of this taxon name
+ * and keeps the nomenclatural rule considered for it. The basionym
+ * relationship will be added to this taxon name and to the basionym.
+ * The basionym cannot have itself a basionym.
+ *
+ * @see #getBasionym()
+ * @see #setBasionym(TaxonNameBase)
+ */
+ public void setBasionym(T basionym, String ruleConsidered){
+ basionym.addRelationshipToName(this, NameRelationshipType.BASIONYM(), ruleConsidered);
}
- //TODO for PROTOTYPE
@Transient
- public INameCacheStrategy getCacheStrategy() {
- return cacheStrategy;
- }
- public void setCacheStrategy(INameCacheStrategy cacheStrategy) {
- this.cacheStrategy = cacheStrategy;
- }
+ public abstract S getCacheStrategy();
+ public abstract void setCacheStrategy(S cacheStrategy);
+ /**
+ * Returns the taxonomic {@link Rank rank} of this taxon name.
+ *
+ * @see Rank
+ */
@ManyToOne
- @Cascade({CascadeType.SAVE_UPDATE})
+ //@Cascade({CascadeType.SAVE_UPDATE})
public Rank getRank(){
return this.rank;
}
+ /**
+ * @see #getRank()
+ */
public void setRank(Rank rank){
this.rank = rank;
}
+ /**
+ * Returns the {@link reference.INomenclaturalReference nomenclatural reference} of this taxon name.
+ * The nomenclatural reference is here meant to be the one publication
+ * this taxon name was originally published in while fulfilling the formal
+ * requirements as specified by the corresponding nomenclatural code.
+ *
+ * @see reference.INomenclaturalReference
+ * @see reference.ReferenceBase
+ */
@ManyToOne
@Cascade({CascadeType.SAVE_UPDATE})
- public ReferenceBase getNomenclaturalReference(){
- return (ReferenceBase) this.nomenclaturalReference;
+ @Target(ReferenceBase.class)
+ public INomenclaturalReference getNomenclaturalReference(){
+ return (INomenclaturalReference) this.nomenclaturalReference;
}
+ /**
+ * Assigns a nomenclatural {@link reference.INomenclaturalReference nomenclatural reference} to this taxon name.
+ * The corresponding {@link reference.ReferenceBase.isNomenclaturallyRelevant nomenclaturally relevant flag} will be set to true
+ * as it is obviously used for nomenclatural purposes.
+ *
+ * @see #getNomenclaturalReference()
+ */
public void setNomenclaturalReference(INomenclaturalReference nomenclaturalReference){
this.nomenclaturalReference = nomenclaturalReference;
}
-
+ /**
+ * Returns the appended phrase string assigned to this taxon name.
+ * The appended phrase is a non-atomised addition to a name. It is
+ * not ruled by a nomenclatural code.
+ */
public String getAppendedPhrase(){
return this.appendedPhrase;
}
+ /**
+ * @see #getAppendedPhrase()
+ */
public void setAppendedPhrase(String appendedPhrase){
this.appendedPhrase = appendedPhrase;
}
+ /**
+ * Returns the details string of the nomenclatural reference assigned
+ * to this taxon name. The details describe the exact localisation within
+ * the publication used as nomenclature reference. These are mostly
+ * (implicitly) pages but can also be figures or tables or any other
+ * element of a publication. A nomenclatural micro reference (details)
+ * requires the existence of a nomenclatural reference.
+ */
+ //Details of the nomenclatural reference (protologue).
public String getNomenclaturalMicroReference(){
return this.nomenclaturalMicroReference;
}
+ /**
+ * @see #getNomenclaturalMicroReference()
+ */
public void setNomenclaturalMicroReference(String nomenclaturalMicroReference){
this.nomenclaturalMicroReference = nomenclaturalMicroReference;
}
+ /**
+ * Returns the boolean value of the flag indicating whether the used {@link eu.etaxonomy.cdm.strategy.parser.INonViralNameParser parser}
+ * method was able to parse the taxon name string successfully (false)
+ * or not (true). The parser itself may also depend on the {@link NomenclaturalCode nomenclatural code}
+ * governing the construction of this taxon name.
+ *
+ * @return the boolean value of the hasProblem flag
+ * @see #getNameCache()
+ */
public boolean getHasProblem(){
return this.hasProblem;
}
+ /**
+ * @see #getHasProblem()
+ */
public void setHasProblem(boolean hasProblem){
this.hasProblem = hasProblem;
}
+ /**
+ * Returns exactly the same boolean value as the {@link #getHasProblem() getHasProblem} method.
+ *
+ * @see #getHasProblem()
+ */
+ public boolean hasProblem(){
+ return getHasProblem();
+ }
+ /**
+ * Returns the set of {@link NameTypeDesignation name type designations} assigned
+ * to this taxon name the rank of which must be above "species".
+ * The name type designations include all the taxon names used to typify
+ * this name and eventually the rejected or conserved status
+ * of these designations.
+ *
+ * @see NameTypeDesignation
+ * @see SpecimenTypeDesignation
+ */
@OneToMany
- @Cascade({CascadeType.SAVE_UPDATE, CascadeType.DELETE_ORPHAN})
+ //TODO @Cascade({CascadeType.SAVE_UPDATE, CascadeType.DELETE_ORPHAN})
+ @Cascade(CascadeType.SAVE_UPDATE)
public Set<NameTypeDesignation> getNameTypeDesignations() {
return nameTypeDesignations;
}
+ /**
+ * @see #getNameTypeDesignations()
+ */
protected void setNameTypeDesignations(Set<NameTypeDesignation> nameTypeDesignations) {
this.nameTypeDesignations = nameTypeDesignations;
}
+
- public void addTypeDesignation(TaxonNameBase typeSpecies, ReferenceBase citation, String citationMicroReference, String originalNameString, boolean isRejectedType, boolean isConservedType) {
+ /**
+ * Creates and adds a new {@link NameTypeDesignation name type designation}
+ * to this taxon name's set of name type designations.
+ *
+ * @param typeSpecies the taxon name to be used as type of this taxon name
+ * @param citation the reference for this new designation
+ * @param citationMicroReference the string with the details (generally pages) within the reference
+ * @param originalNameString the taxon name used in the reference to assert this designation
+ * @param isRejectedType the boolean status for rejected
+ * @param isConservedType the boolean status for conserved
+ * @see #getNameTypeDesignations()
+ * @see #addTypeDesignation(Specimen, TypeDesignationStatus, ReferenceBase, String, String)
+ */
+ public void addNameTypeDesignation(TaxonNameBase typeSpecies, ReferenceBase citation, String citationMicroReference, String originalNameString, boolean isRejectedType, boolean isConservedType) {
NameTypeDesignation td = new NameTypeDesignation(this, typeSpecies, citation, citationMicroReference, originalNameString, isRejectedType, isConservedType);
}
- public void addTypeDesignation(Specimen typeSpecimen, TypeDesignationStatus status, ReferenceBase citation, String citationMicroReference, String originalNameString) {
- this.homotypicalGroup.addTypeDesignation(typeSpecimen, status, citation, citationMicroReference, originalNameString);
- }
- public void removeTypeDesignation(NameTypeDesignation typeDesignation) {
+
+ /**
+ * Removes one element from the set of {@link NameTypeDesignation name type designations} of this taxon name.
+ * The name type designation itself will be nullified.
+ *
+ * @param typeDesignation the name type designation of this taxon name which should be deleted
+ * @see #getNameTypeDesignations()
+ * @see #removeTypeDesignation(SpecimenTypeDesignation)
+ */
+ public void removeNameTypeDesignation(NameTypeDesignation typeDesignation) {
+ //TODO
+ logger.warn("not yet fully implemented: nullify the name type designation itself?");
this.nameTypeDesignations.remove(typeDesignation);
}
+
+ /**
+ * @return the specimenTypeDesignations
+ */
+ @ManyToMany
+ @Cascade(CascadeType.SAVE_UPDATE)
+ public Set<SpecimenTypeDesignation> getSpecimenTypeDesignations() {
+ return specimenTypeDesignations;
+ }
+ /**
+ * @param specimenTypeDesignations the specimenTypeDesignations to set
+ */
+ protected void setSpecimenTypeDesignations(Set<SpecimenTypeDesignation> specimenTypeDesignations) {
+ this.specimenTypeDesignations = specimenTypeDesignations;
+ }
+
+ /**
+ * Returns the set of {@link SpecimenTypeDesignation specimen type designations} assigned
+ * indirectly to this taxon name through its {@link HomotypicalGroup homotypical group}.
+ * The rank of this taxon name is generally "species" or below.
+ * The specimen type designations include all the specimens on which
+ * the typification of this name is based (and which are common to all
+ * taxon names belonging to the homotypical group) and eventually
+ * the status of these designations.
+ *
+ * @see SpecimenTypeDesignation
+ * @see NameTypeDesignation
+ */
+ @Transient
+ public Set<SpecimenTypeDesignation> getSpecimenTypeDesignationsOfHomotypicalGroup() {
+ return this.getHomotypicalGroup().getTypeDesignations();
+ }
+
+ /**
+ * Adds a new {@link SpecimenTypeDesignation specimen type designation}
+ * to the set of specimen type designations assigned to the
+ * {@link HomotypicalGroup homotypical group} to which this taxon name belongs.
+ *
+ * @param typeSpecimen the specimen to be used as a type for this taxon name's homotypical group
+ * @param status the specimen type designation status
+ * @param citation the reference for this new specimen type designation
+ * @param citationMicroReference the string with the details (generally pages) within the reference
+ * @param originalNameString the taxon name used in the reference to assert this designation
+ * @see HomotypicalGroup#getTypeDesignations()
+ * @see #addTypeDesignation(TaxonNameBase, ReferenceBase, String, String, boolean, boolean)
+ * @see TypeDesignationStatus
+ */
+ public void addSpecimenTypeDesignation(Specimen typeSpecimen, TypeDesignationStatus status, ReferenceBase citation, String citationMicroReference, String originalNameString, boolean addToAllNames) {
+ SpecimenTypeDesignation specimenTypeDesignation =
+ SpecimenTypeDesignation.NewInstance(typeSpecimen, status, citation, citationMicroReference, originalNameString);
+ this.getHomotypicalGroup().addTypeDesignation(specimenTypeDesignation, addToAllNames);
+ }
+
+ //only to be used for xxx
+ protected void addSpecimenTypeDesignation(SpecimenTypeDesignation specimenTypeDesignation) {
+ this.specimenTypeDesignations.add(specimenTypeDesignation);
+ }
+
+ //only to be used for xxx
+ protected void removeSpecimenTypeDesignation(SpecimenTypeDesignation specimenTypeDesignation) {
+ this.specimenTypeDesignations.remove(specimenTypeDesignation);
+ }
+
+ /**
+ * Removes one element from the set of {@link SpecimenTypeDesignation specimen type designations} assigned to the
+ * {@link HomotypicalGroup homotypical group} to which this taxon name belongs.
+ * The specimen type designation itself will be nullified.
+ *
+ * @param typeDesignation the specimen type designation which should be deleted
+ * @see HomotypicalGroup#getTypeDesignations()
+ * @see #removeTypeDesignation(NameTypeDesignation)
+ */
public void removeTypeDesignation(SpecimenTypeDesignation typeDesignation) {
+ logger.warn("not yet fully implemented: nullify the specimen type designation itself?");
this.homotypicalGroup.removeTypeDesignation(typeDesignation);
}
-
+ /**
+ * Returns the {@link HomotypicalGroup homotypical group} to which
+ * this taxon name belongs. A homotypical group represents all taxon names
+ * that share the same type specimens.
+ *
+ * @see HomotypicalGroup
+ */
@ManyToOne
@Cascade({CascadeType.SAVE_UPDATE})
public HomotypicalGroup getHomotypicalGroup() {
return homotypicalGroup;
}
- public void setHomotypicalGroup(HomotypicalGroup newHomotypicalGroup) {
- if(this.homotypicalGroup == newHomotypicalGroup) return;
- if (homotypicalGroup != null) {
- homotypicalGroup.typifiedNames.remove(this);
- }
- if (newHomotypicalGroup!= null) {
- newHomotypicalGroup.typifiedNames.add(this);
- }
+ @Deprecated //only for bidirectional and persistence use
+ protected void setHomotypicalGroup(HomotypicalGroup newHomotypicalGroup) {
this.homotypicalGroup = newHomotypicalGroup;
}
@Transient
public StrictReferenceBase getCitation(){
+ //TODO What is the purpose of this method differing from the getNomenclaturalReference method?
+ logger.warn("getCitation not yet implemented");
return null;
}
+ /**
+ * Returns the complete string containing the
+ * {@link reference.INomenclaturalReference#getNomenclaturalCitation() nomenclatural reference citation}
+ * (including {@link #getNomenclaturalMicroReference() details}) assigned to this taxon name.
+ *
+ * @see reference.INomenclaturalReference#getNomenclaturalCitation()
+ * @see #getNomenclaturalReference()
+ * @see #getNomenclaturalMicroReference()
+ */
@Transient
public String getCitationString(){
+ logger.warn("getCitationString not yet implemented");
return null;
}
@Transient
public String[] getProblems(){
+ logger.warn("getProblems not yet implemented");
return null;
}
/**
- * returns year of according nomenclatural reference, null if nomenclatural
- * reference does not exist
+ * Returns the string containing the publication date (generally only year)
+ * of the nomenclatural reference, null if there is no nomenclatural
+ * reference.
+ *
+ * @see reference.INomenclaturalReference#getYear()
*/
@Transient
- public String getYear(){
- return "";
+ public String getReferenceYear(){
+ if (this.getNomenclaturalReference() != null ){
+ return this.getNomenclaturalReference().getYear();
+ }else{
+ return null;
+ }
}
+ /**
+ * Returns the set of {@link taxon.TaxonBase taxon bases} that refer to this taxon name.
+ * In this context a taxon base means the use of a taxon name by a reference
+ * either as a taxon ("accepted/correct" name) or as a (junior) synonym.
+ * A taxon name can be used by several distinct references but only once
+ * within a taxonomic treatment (identified by one reference).
+ *
+ * @see taxon.TaxonBase
+ * @see #getTaxa()
+ * @see #getSynonyms()
+ */
+ @OneToMany(mappedBy="name", fetch= FetchType.EAGER)
+ public Set<TaxonBase> getTaxonBases() {
+ return this.taxonBases;
+ }
+ /**
+ * @see #getTaxonBases()
+ */
+ protected void setTaxonBases(Set<TaxonBase> taxonBases) {
+ if (taxonBases == null){
+ taxonBases = new HashSet<TaxonBase>();
+ }else{
+ this.taxonBases = taxonBases;
+ }
+ }
+ /**
+ * Adds a new {@link taxon.TaxonBase taxon base}
+ * to the set of taxon bases using this taxon name.
+ *
+ * @param taxonBase the taxon base to be added
+ * @see #getTaxonBases()
+ */
+ //TODO protected
+ public void addTaxonBase(TaxonBase taxonBase){
+ taxonBases.add(taxonBase);
+ initMethods();
+ invokeSetMethod(methodTaxonBaseSetName, taxonBase);
+ }
+ public void removeTaxonBase(TaxonBase taxonBase){
+ taxonBases.remove(taxonBase);
+ initMethods();
+ invokeSetMethodWithNull(methodTaxonBaseSetName, taxonBase);
+ }
+
+ private void initMethods(){
+ if (methodTaxonBaseSetName == null){
+ try {
+ methodTaxonBaseSetName = TaxonBase.class.getDeclaredMethod("setName", TaxonNameBase.class);
+ methodTaxonBaseSetName.setAccessible(true);
+ } catch (Exception e) {
+ e.printStackTrace();
+ //TODO handle exception
+ }
+ }
+ }
+
+
/**
+ * Returns the set of {@link taxon.Taxon taxa} ("accepted/correct" names according to any
+ * reference) that are based on this taxon name. This set is a subset of
+ * the set returned by getTaxonBases().
*
- * @param fullname fullname
+ * @see taxon.Taxon
+ * @see #getTaxonBases()
+ * @see #getSynonyms()
*/
- public boolean parseName(String fullname){
+ @Transient
+ public Set<Taxon> getTaxa(){
+ Set<Taxon> result = new HashSet<Taxon>();
+ for (TaxonBase taxonBase : this.taxonBases){
+ if (taxonBase instanceof Taxon){
+ result.add((Taxon)taxonBase);
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Returns the set of {@link taxon.Synonym (junior) synonyms} (according to any
+ * reference) that are based on this taxon name. This set is a subset of
+ * the set returned by getTaxonBases().
+ *
+ * @see taxon.Synonym
+ * @see #getTaxonBases()
+ * @see #getTaxa()
+ */
+ @Transient
+ public Set<Synonym> getSynonyms() {
+ Set<Synonym> result = new HashSet<Synonym>();
+ for (TaxonBase taxonBase : this.taxonBases){
+ if (taxonBase instanceof Synonym){
+ result.add((Synonym)taxonBase);
+ }
+ }
+ return result;
+ }
+
+// ***********
+ /**
+ * Returns the boolean value indicating whether a given taxon name belongs
+ * to the same {@link HomotypicalGroup homotypical group} as this taxon name (true)
+ * or not (false). Returns "true" only if the homotypical groups of both
+ * taxon names exist and if they are identical.
+ *
+ * @param homoTypicName the taxon name the homotypical group of which is to be checked
+ * @return the boolean value of the check
+ * @see HomotypicalGroup
+ */
+ public boolean isHomotypic(TaxonNameBase homoTypicName) {
+ if (homoTypicName == null) {
+ return false;
+ }
+ HomotypicalGroup homotypicGroup = homoTypicName.getHomotypicalGroup();
+ if (homotypicGroup == null || this.getHomotypicalGroup() == null) {
+ return false;
+ }
+ if (homotypicGroup.equals(this.getHomotypicalGroup())) {
+ return true;
+ }
return false;
- }
+ }
+
+
+//********* Rank comparison shortcuts ********************//
/**
- * Return a set of taxa that use this name
- * @return
+ * Returns the boolean value indicating whether the taxonomic rank of this
+ * taxon name is higher than the genus rank (true) or not (false).
+ * Suprageneric non viral names are monomials.
+ *
+ * @see #isGenus()
+ * @see #isInfraGeneric()
+ * @see #isSpecies()
+ * @see #isInfraSpecific()
*/
- public Set<Taxon> getTaxa(){
- // TODO: implement this method via bidirectional TaxonBase-NameBase relation or use a DAO instead
- return null;
+ @Transient
+ public boolean isSupraGeneric() {
+ return getRank().isSupraGeneric();
}
/**
- * Return a set of synonyms that use this name
- * @return
+ * Returns the boolean value indicating whether the taxonomic rank of this
+ * taxon name is the genus rank (true) or not (false). Non viral names with
+ * genus rank are monomials.
+ *
+ * @see #isSupraGeneric()
+ * @see #isInfraGeneric()
+ * @see #isSpecies()
+ * @see #isInfraSpecific()
*/
- public Set<Synonym> getSynonyms(){
- // TODO: implement this method via bidirectional TaxonBase-NameBase relation or use a DAO instead
- return null;
+ @Transient
+ public boolean isGenus() {
+ return getRank().isGenus();
+ }
+ /**
+ * Returns the boolean value indicating whether the taxonomic rank of this
+ * taxon name is higher than the species rank and lower than
+ * the genus rank (true) or not (false). Infrageneric non viral names
+ * are binomials.
+ *
+ * @see #isSupraGeneric()
+ * @see #isGenus()
+ * @see #isSpecies()
+ * @see #isInfraSpecific()
+ */
+ @Transient
+ public boolean isInfraGeneric() {
+ return getRank().isInfraGeneric();
+ }
+ /**
+ * Returns the boolean value indicating whether the taxonomic rank of this
+ * taxon name is the species rank (true) or not (false). Non viral names
+ * with species rank are binomials.
+
+ *
+ * @see #isSupraGeneric()
+ * @see #isGenus()
+ * @see #isInfraGeneric()
+ * @see #isInfraSpecific()
+ */
+ @Transient
+ public boolean isSpecies() {
+ return getRank().isSpecies();
}
+ /**
+ * Returns the boolean value indicating whether the taxonomic rank of this
+ * taxon name is lower than the species rank (true) or not (false).
+ * Infraspecific non viral names are trinomials.
+ *
+ * @see #isSupraGeneric()
+ * @see #isGenus()
+ * @see #isInfraGeneric()
+ * @see #isSpecies()
+ */
+ @Transient
+ public boolean isInfraSpecific() {
+ return getRank().isInfraSpecific();
+ }
+
+
+ /**
+ * Returns the {@link NomenclaturalCode nomenclatural code} that governs
+ * the construction of this taxon name. Each taxon name is governed by one
+ * and only one nomenclatural code.
+ *
+ * @see #isCodeCompliant()
+ * @see #getHasProblem()
+ */
+ @Transient
+ abstract public NomenclaturalCode getNomeclaturalCode();
+
+
+
}
\ No newline at end of file
BGBM BDI Projects / cdmlib.git / blobdiff